IGEM:Melbourne/2008/BCModelling/ModelDevelopment

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Calibration

Strategy for completion described below

• connections - this is the first part of the modelling to get the connections right both biologically and theoretically. Jason and Dave are doing this for the linear and binary model respectively. Include as much as possible, remember to employ special cases to be able to simplify the model when necessary and ensure complexity when required.

• parameters - obtain the right parameters for Hill functions, Kd, degradation rates, RL/RK binding constants, and other parameters for more complex models (such as [REFshae 1985|shae 1985], statisical mechanics model for promoter activity)

• break apart - need to obtain realistic and desired output for each bit of the binary or each component of the linear model.
  • To assist the individual circuits are to be 'broken down' into smaller section that will be have parameters adjusted such that they behave in two deisred fashions: ideal (as close to square-wave as possible) and real not changing the estimated parameters.

• iterate to optimize results...

Initial Model Assumptions

• (refer to arkin 1998(REF) paper here ...
• deterministic chemical kinetics
• inital concentrations of intermediates at 0
• only model chemical interactions and focus on transcriptional control, ignoring post-transcriptional control mechanisms and characterise protein production as a continuous process.